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- PDB-4no5: Crystal structure of non-phosphorylated form of AMPD2 phosphopept... -

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Basic information

Entry
Database: PDB / ID: 4no5
TitleCrystal structure of non-phosphorylated form of AMPD2 phosphopeptide bound to HLA-A2
Components
  • AMP deaminase 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM/ANTIGEN / Nonphosphorylated peptide / peptide-MHC complex / MHC / peptide conformation / tumor immunology / post translational modification / tumor antigens / IMMUNE SYSTEM-ANTIGEN complex
Function / homology
Function and homology information


cyclic purine nucleotide metabolic process / AMP deaminase / AMP deaminase activity / IMP biosynthetic process / podocyte development / AMP metabolic process / Purine salvage / IMP salvage / GTP metabolic process / positive regulation of memory T cell activation ...cyclic purine nucleotide metabolic process / AMP deaminase / AMP deaminase activity / IMP biosynthetic process / podocyte development / AMP metabolic process / Purine salvage / IMP salvage / GTP metabolic process / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell receptor binding / ATP metabolic process / energy homeostasis / negative regulation of receptor binding / cholesterol homeostasis / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane
Similarity search - Function
AMP deaminase / AMP deaminase / Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Metal-dependent hydrolase / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains ...AMP deaminase / AMP deaminase / Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Metal-dependent hydrolase / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / AMP deaminase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsMohammed, F. / Stones, D.H. / Willcox, B.E.
CitationJournal: Oncotarget / Year: 2017
Title: The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status.
Authors: Mohammed, F. / Stones, D.H. / Zarling, A.L. / Willcox, C.R. / Shabanowitz, J. / Cummings, K.L. / Hunt, D.F. / Cobbold, M. / Engelhard, V.H. / Willcox, B.E.
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: AMP deaminase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7877
Polymers44,5773
Non-polymers2094
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-14 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.400, 79.300, 56.800
Angle α, β, γ (deg.)90.000, 115.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2 / Class I histocompatibility antigen A*0201


Mass: 31854.203 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 25-299)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11635.002 Da / Num. of mol.: 1 / Fragment: UNP residues 22-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide AMP deaminase 2


Mass: 1088.258 Da / Num. of mol.: 1 / Fragment: peptide (UNP residues 165-173) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01433

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Non-polymers , 3 types, 269 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 19% PEG3350, 0.1 M Bis-Tris propane, 0.1 M sodium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.101→19.891 Å / Num. obs: 26307 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 20.796 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 25.24
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.101-2.40.2411.35942878581198.8
2.4-2.70.15516.68603375261199.8
2.7-30.10822.05388763358199.7
3-40.05737.54610765253199.7
4-50.03954.54218401873199.6
5-60.04251.759779840199.2
6-100.04550.9910517913199.3
10-19.8910.03867.252415228186.7

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BH9

3bh9


Resolution: 2.101→19.89 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / WRfactor Rfree: 0.2099 / WRfactor Rwork: 0.1699 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8547 / SU B: 4.389 / SU ML: 0.119 / SU R Cruickshank DPI: 0.2193 / SU Rfree: 0.1866 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 1272 4.8 %RANDOM
Rwork0.1878 ---
obs0.1901 26305 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 38.37 Å2 / Biso mean: 14.1871 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.101→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 13 265 3422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213227
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.9214375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2095379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79823.046174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84415516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5551529
X-RAY DIFFRACTIONr_chiral_restr0.080.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212544
X-RAY DIFFRACTIONr_mcbond_it0.5511.51901
X-RAY DIFFRACTIONr_mcangle_it1.08623061
X-RAY DIFFRACTIONr_scbond_it1.7331326
X-RAY DIFFRACTIONr_scangle_it2.9434.51314
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 85 -
Rwork0.207 1781 -
all-1866 -
obs--97.39 %

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